Package index • divent

Package summary

divent divent-package: divent

Datasets

paracou_6_abd paracou_6_wmppp: Paracou plot 6

paracou_6_fundist: Functional distances between Paracou plot 6 species

paracou_6_taxo: Taxonomy of Paracou plot 6 species

mock_3sp_abd mock_3sp_dist mock_3sp_tree: Mock data

non_species_columns: Non-Species columns

Generate data

rcommunity() rspcommunity(): Random communities

rlseries(): Log-Series Distribution

Diversity

div_gen_simpson(): Generalized Simpson's Diversity

div_hill(): Hill number of a Community

div_hurlbert(): Hurlbert Diversity of a Community

div_part(): Diversity partition

div_pd(): Faith's Phylogenetic Diversity of a Community

div_phylo(): Phylogenetic Diversity of a Community

div_richness(): Number of Species of a Community

div_similarity(): Similarity-Based Diversity of a Community

Entropy

ent_allen(): Allen et al.'s Phylogenetic Entropy of a Community

ent_gen_simpson(): Generalized Simpson's Entropy

ent_hurlbert(): Hurlbert Entropy of a Community

ent_phylo(): Phylogenetic Entropy of a Community

ent_rao(): Rao's Quadratic Entropy of a Community

ent_shannon(): Shannon's Entropy of a Community

ent_similarity(): Similarity-Based Entropy of a Community

ent_simpson(): Simpson's Entropy of a Community

ent_sp_simpson() ent_sp_simpsonEnvelope(): Spatially Explicit Simpson's Entropy

ent_tsallis(): Tsallis Entropy of a Community

Diversity accumulations

accum_ent_phylo() accum_div_phylo(): Phylogenetic Diversity Accumulation of a Community

accum_tsallis() accum_hill(): Diversity Accumulation of a Community

plot(<accum_sp>) autoplot(<accum_sp>) plot_map(): Spatial Accumulation of Diversity

accum_sp_tsallis() accum_sp_hill() accum_mixing(): Spatial Diversity Accumulation of a Community

Diversity profiles

profile_hill(): Diversity Profile of a Community

profile_phylo(): Phylogenetic Diversity Profile of a Community

profile_similarity(): Similarity-Based Diversity Profile of a Community

Functional features

fun_ordinariness(): Functional ordinariness of a community

fun_similarity(): Functional similarity

Plots

plot(<accum_sp>) autoplot(<accum_sp>) plot_map(): Spatial Accumulation of Diversity

autoplot(<accumulation>): Plot Accumulation Objects

autoplot(<profile>): Plot Profile Objects

autoplot(<wmppp>): ggplot method to plot wmppp objects

plot(<species_distribution>) autoplot(<species_distribution>): Plot Profile Objects

plot(<phylo_divent>): Plot phylo_divent Objects

Statistics from species distributions

abd_freq_count(): Abundance Frequency Count of a Community

abd_species() abd_sum() prob_species(): Abundances of Communities

coverage() coverage_to_size(): Sample Coverage of a Community

fit_rac(): Fit a distribution

Classes

species_distribution() as_species_distribution() is_species_distribution() as_probabilities() is_probabilities() abundances() as_abundances() is_abundances() as.matrix(<species_distribution>) as.double(<species_distribution>) as.numeric(<species_distribution>): Species Distributions

probabilities(): Probabilities of Species

as_phylo_divent() is_phylo_divent(): Class phylo_divent

Utilities

exp_q(): Deformed exponential

ln_q(): Deformed logarithm

e_n_q(): Grassberger's expectation of n^q

metacommunity(): Aggregate communities into a metacommunity

alphahull(): alpha-shape calculation